Merge pull request #12 from Muster-Suchen-und-Erkennen/update-depende…

…ncies

Update dependencies

docs/conf.py

@@ -91,9 +91,9 @@
 autosectionlabel_prefix_document = False
 autosectionlabel_maxdepth = None
 
-intersphinx_mapping: Optional[
-    Dict[str, Tuple[str, Union[Optional[str], Tuple[str]]]]
-] = None
+intersphinx_mapping: Optional[Dict[str, Tuple[str, Union[Optional[str], Tuple[str]]]]] = (
+    None
+)
 intersphinx_timeout = 30
 
 source_suffix = {

migrations/env.py

@@ -3,10 +3,8 @@
 import logging
 from logging.config import fileConfig
 
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
-
 from alembic import context
+from sqlalchemy import engine_from_config, pool
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -23,9 +21,8 @@
 # target_metadata = mymodel.Base.metadata
 from flask import current_app
 
-current_app.config[
-    "SQLITE_FOREIGN_KEYS"
-] = False  # do NOT use foreign key checking when updating DB
+# do NOT use foreign key checking when updating DB
+current_app.config["SQLITE_FOREIGN_KEYS"] = False
 config.set_main_option(
     "sqlalchemy.url",
     str(current_app.extensions["migrate"].db.engine.url).replace("%", "%%"),
@@ -84,13 +81,17 @@ def process_revision_directives(context, revision, directives):
     )
 
     with connectable.connect() as connection:
+        extra_kwargs = dict(current_app.extensions["migrate"].configure_args)
+        # remove duplicate args from extra config
+        extra_kwargs.pop("compare_type", None)
+        extra_kwargs.pop("render_as_batch", None)
         context.configure(
             connection=connection,
             target_metadata=target_metadata,
             process_revision_directives=process_revision_directives,
             render_as_batch=True,
             compare_type=True,
-            **current_app.extensions["migrate"].configure_args
+            **extra_kwargs,
         )
 
         with context.begin_transaction():

migrations/versions/a18bebd2bb1a_initial_migration.py

@@ -3,6 +3,7 @@
 Revision ID: a18bebd2bb1a
 Create Date: 2021-09-19 20:16:31.258752
 """
+
 from alembic import op
 import sqlalchemy as sa
 

muse_for_anything/api/util.py

@@ -1,4 +1,5 @@
 """Module containing utilities for flask smorest APIs."""
+
 from typing import Any, Dict
 from flask import url_for
 from flask_smorest import Blueprint

muse_for_anything/api/v1_api/generators/namespace.py

@@ -335,7 +335,9 @@ def generate_api_object(
             return
 
         return NamespaceData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,

muse_for_anything/api/v1_api/generators/object.py

@@ -248,7 +248,9 @@ def generate_api_object(
             return
 
         return ObjectData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,

muse_for_anything/api/v1_api/generators/object_version.py

@@ -158,9 +158,7 @@ def update_key(
         return key
 
 
-class ObjectVersionSelfLinkGenerator(
-    LinkGenerator, resource_type=OntologyObjectVersion
-):
+class ObjectVersionSelfLinkGenerator(LinkGenerator, resource_type=OntologyObjectVersion):
     def generate_link(
         self,
         resource: OntologyObjectVersion,
@@ -199,7 +197,9 @@ def generate_api_object(
             return
 
         return ObjectData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,

muse_for_anything/api/v1_api/generators/taxonomy.py

@@ -194,7 +194,9 @@ def generate_api_object(
             return
 
         return TaxonomyData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,

muse_for_anything/api/v1_api/generators/taxonomy_item.py

@@ -447,7 +447,9 @@ def generate_api_object(
         ]
 
         return TaxonomyItemData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             sort_key=resource.sort_key,

muse_for_anything/api/v1_api/generators/taxonomy_item_relation.py

@@ -318,7 +318,9 @@ def generate_api_object(
             return
 
         return TaxonomyItemRelationData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             source_item=LinkGenerator.get_link_of(resource.taxonomy_item_source),
             target_item=LinkGenerator.get_link_of(resource.taxonomy_item_target),
             created_on=resource.created_on,

muse_for_anything/api/v1_api/generators/taxonomy_item_version.py

@@ -282,7 +282,9 @@ def generate_api_object(
         ]
 
         return TaxonomyItemData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             sort_key=resource.sort_key,

muse_for_anything/api/v1_api/generators/user_management.py

@@ -253,7 +253,9 @@ def generate_link(
             return
         link = LinkGenerator.get_link_of(CollectionResource(UserRole, resource=resource))
         link.rel = (CREATE_REL, POST_REL, REQUIRES_FRESH_LOGIN_REL)
-        link.schema = url_for(SCHEMA_RESOURCE, schema_id=USER_ROLE_POST_SCHEMA, _external=True)
+        link.schema = url_for(
+            SCHEMA_RESOURCE, schema_id=USER_ROLE_POST_SCHEMA, _external=True
+        )
         return link
 
 
@@ -271,7 +273,9 @@ def generate_api_object(
             return
 
         return UserData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             username=resource.username,
             e_mail=resource.e_mail,
         )

muse_for_anything/api/v1_api/models/ontology.py

@@ -48,7 +48,9 @@ class DeletedPageSchemaMixin:
     deleted = ma.fields.Boolean(required=False, allow_none=True, missing=False)
 
 
-class NamespacePageParamsSchema(SearchPageSchemaMixin, DeletedPageSchemaMixin, CursorPageArgumentsSchema):
+class NamespacePageParamsSchema(
+    SearchPageSchemaMixin, DeletedPageSchemaMixin, CursorPageArgumentsSchema
+):
     pass
 
 
@@ -128,11 +130,15 @@ class FileExportData(BaseApiObject):
     content_type: str = "application/xml"
 
 
-class ObjectTypePageParamsSchema(CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin):
+class ObjectTypePageParamsSchema(
+    CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin
+):
     pass
 
 
-class ObjectTypeVersionsPageParamsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin):
+class ObjectTypeVersionsPageParamsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin
+):
     pass
 
 
@@ -171,15 +177,21 @@ class ObjectData(BaseApiObject, ChangesDataMixin, NameDescriptionMixin):
     data: Any
 
 
-class ObjectsCursorPageArgumentsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin, SearchPageSchemaMixin):
+class ObjectsCursorPageArgumentsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin, SearchPageSchemaMixin
+):
     type_id = ma.fields.String(data_key="type-id", allow_none=True, load_only=True)
 
 
-class ObjectVersionsCursorPageArgumentsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin):
+class ObjectVersionsCursorPageArgumentsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin
+):
     pass
 
 
-class TaxonomyPageParamsSchema(CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin):
+class TaxonomyPageParamsSchema(
+    CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin
+):
     pass
 
 
@@ -200,11 +212,15 @@ class TaxonomyData(BaseApiObject, ChangesDataMixin, NameDescriptionMixin):
     items: Sequence[ApiLink] = tuple()
 
 
-class TaxonomyItemPageParamsSchema(CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin):
+class TaxonomyItemPageParamsSchema(
+    CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin
+):
     pass
 
 
-class TaxonomyItemVersionsPageParamsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin):
+class TaxonomyItemVersionsPageParamsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin
+):
     pass
 
 

muse_for_anything/api/v1_api/namespace.py

@@ -1,6 +1,6 @@
 """Module containing the namespace API endpoints of the v1 API."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 from http import HTTPStatus
 from typing import Any, List, Optional
 
@@ -396,7 +396,7 @@ def delete(self, namespace: str):
         # only actually delete when not already deleted
         if found_namespace.deleted_on is None:
             # soft delete namespace
-            found_namespace.deleted_on = datetime.utcnow()
+            found_namespace.deleted_on = datetime.now(timezone.utc)
             DB.session.add(found_namespace)
             DB.session.commit()
 

muse_for_anything/api/v1_api/ontology_object_validation.py

@@ -2,9 +2,10 @@
 
 from dataclasses import dataclass
 
+from urllib.parse import urlparse
+
 from muse_for_anything.db.models.taxonomies import TaxonomyItem
-from flask.globals import _request_ctx_stack
-from werkzeug.urls import url_parse
+from flask.globals import request_ctx
 from werkzeug.routing import MapAdapter
 
 from http import HTTPStatus
@@ -36,12 +37,18 @@ class ObjectMetadata:
 def resolve_type_version_schema_url(url_string: str):
     """Resolver url references without creating any http request by directly querying the database."""
     # TODO use url cache
-    url = url_parse(url_string)
+    url = urlparse(url_string)
     # url should already be from a validated type!
-    ctx = _request_ctx_stack.top
-    if ctx is None:
+    try:
+        ctx = request_ctx._get_current_object()
+    except RuntimeError:
         raise DataVisitorException("No request context to check schema url against!")
-    url_adapter: MapAdapter = ctx.url_adapter
+    url_adapter: Optional[MapAdapter] = ctx.url_adapter
+    if url_adapter is None:
+        raise DataVisitorException(
+            "No url adapter found in request context! Unable to check URL."
+            f"URL: '{url}'"
+        )
     if url.netloc != url_adapter.get_host(None):
         raise DataVisitorException(
             "Only references to schemas on the same MUSE4Anything instance allowed! "
@@ -62,12 +69,12 @@ def resolve_type_version_schema_url(url_string: str):
     version: str = params.get("version")
     if endpoint == "api-v1.TypeVersionView":
 
-        found_type_version: Optional[
-            OntologyObjectTypeVersion
-        ] = OntologyObjectTypeVersion.query.filter(
-            OntologyObjectTypeVersion.version == int(version),
-            OntologyObjectTypeVersion.object_type_id == int(object_type),
-        ).first()
+        found_type_version: Optional[OntologyObjectTypeVersion] = (
+            OntologyObjectTypeVersion.query.filter(
+                OntologyObjectTypeVersion.version == int(version),
+                OntologyObjectTypeVersion.object_type_id == int(object_type),
+            ).first()
+        )
 
         if found_type_version is None:
             raise DataVisitorException(f"Invalid schema ref! Schema '{url}' not found!")

muse_for_anything/api/v1_api/ontology_objects.py

@@ -1,6 +1,6 @@
 """Module containing the object API endpoints of the v1 API."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 from http import HTTPStatus
 from typing import Any, List, Optional
 
@@ -651,7 +651,7 @@ def delete(self, namespace: str, object_id: str):
         # only actually delete when not already deleted
         if found_object.deleted_on is None:
             # soft delete object
-            found_object.deleted_on = datetime.utcnow()
+            found_object.deleted_on = datetime.now(timezone.utc)
             # TODO soft delete komposition objects (also implement undelete…)
             DB.session.add(found_object)
             DB.session.commit()